core: update cellbase dependency to get the clinical variant client i…

…n order to search load clinical variants into bionetdb
opencb · Apr 16, 2018 · 6289c8b · 6289c8b
1 parent 24d6e51
commit 6289c8b
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Showing 3 changed files with 21 additions and 1 deletion.
diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/BioNetDBManager.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/BioNetDBManager.java
@@ -108,6 +108,11 @@ public void loadVcf(java.nio.file.Path path) throws BioNetDBException {
         neo4JVariantLoader.loadVCFFile(path);
     }
 
+    public void loadClinicalVariant() throws IOException, BioNetDBException {
+        Neo4JVariantLoader neo4JVariantLoader = new Neo4JVariantLoader((Neo4JNetworkDBAdaptor) networkDBAdaptor);
+        neo4JVariantLoader.loadClinivalVariants(cellBaseClient.getClinicalClient());
+    }
+
     public void annotate() {
 
     }

diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JVariantLoader.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JVariantLoader.java
@@ -21,8 +21,12 @@
 import org.opencb.bionetdb.core.network.Node;
 import org.opencb.bionetdb.core.network.Relation;
 import org.opencb.bionetdb.core.utils.NodeBuilder;
+import org.opencb.cellbase.client.rest.ClinicalVariantClient;
+import org.opencb.cellbase.core.api.ClinicalDBAdaptor;
+import org.opencb.commons.datastore.core.*;
 import org.opencb.commons.utils.ListUtils;
 
+import java.io.IOException;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
@@ -70,6 +74,17 @@ public void loadVCFFile(Path path) {
         vcfFileReader.close();
     }
 
+    public void loadClinivalVariants(ClinicalVariantClient clinicalClient) throws IOException {
+        Query query = new Query();
+        query.put(ClinicalDBAdaptor.QueryParams.SOURCE.key(), "clinvar");
+        QueryResponse<Variant> search = clinicalClient.search(query, QueryOptions.empty());
+        for (QueryResult<Variant> queryResult: search.getResponse()) {
+            if (ListUtils.isNotEmpty(queryResult.getResult())) {
+                loadVariants(queryResult.getResult());
+            }
+        }
+    }
+
     public void loadVariants(List<Variant> variants) {
         // First, initialize uidCounter
         uidCounter = networkDBAdaptor.getUidCounter();

diff --git a/pom.xml b/pom.xml
@@ -24,7 +24,7 @@
         <java.version>1.8</java.version>
         <java-common-libs.version>3.7.0-SNAPSHOT</java-common-libs.version>
         <biodata.version>1.4.0-SNAPSHOT</biodata.version>
-        <cellbase.version>4.5.0-rc</cellbase.version>
+        <cellbase.version>4.6.0-SNAPSHOT</cellbase.version>
         <jackson.version>2.8.10</jackson.version>
         <jersey.version>2.23</jersey.version>
         <build.dir>build</build.dir>